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| Status |
Public on Nov 20, 2015 |
| Title |
The conformation of yeast chromosome III is mating type-dependent and controlled by the recombination enhancer |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
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| Summary |
Yeast chromosome III contains the mating type loci that provide a paradigm for long-range interactions between distant loci. Yeast switch mating type by gene conversion between the MAT locus and either of two silent loci (HML or HMR) on opposite ends of the chromosome. This long-range process is mating type-specific so that MATa cells choose HML as template, while MATα cells use HMR. The Recombination Enhancer (RE), located on the left arm regulates this process. One long-standing hypothesis is that switching is guided by mating type-specific, and possibly RE-dependent three-dimensional folding of chromosome III. Here we used Hi-C, 5C, and live cell imaging to characterize the conformation of chromosome III in both mating types in non-switching strains. We discovered a mating type-specific difference in the folding of the left arm: in MATa cells the left arm is located closely to the centromere-proximal portion of the chromosome as well as to MAT, whereas it is more extended away in MATα cells. Deletion analysis showed that a 1 kb subregion within the RE, which is not necessary during switching, abolished mating type-dependent chromosome folding. In this mutant the conformation of chromosome III is the same in both mating types, but distinct from the wild type MATa or MATα conformations, indicating that the RE induces conformational changes in both mating types. The RE is therefore a composite element with one subregion essential for selecting the appropriate donor during switching, and a separate region involved in modulating chromosome conformation prior to switching.
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| Overall design |
This submission contain 2 biological replicates of Hi-C experiments done in MATa and MATalpha cells in Saccharamycese cerevisiae. It also contains 3 biological replicates of 13 5C experiments in various mutants in MATa and MATalpha cells.
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| Contributor(s) |
Belton J, Lajoie BR, Audibert S, Cantaloube S, Lassadi I, Goiffon I, Baù D, Marti-Renom MA, Bystricky K, Dekker J |
| Citation(s) |
26655901 |
| Submission date |
Oct 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bryan R Lajoie |
| E-mail(s) |
bryan.lajoie@gmail.com
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| Organization name |
UMMS
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| Department |
Program in Systems Biology
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| Lab |
Dekker Lab
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| Street address |
368 Plantation St.
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| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platforms (2) |
| GPL13272 |
Illumina Genome Analyzer IIx (Saccharomyces cerevisiae) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (43)
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| Relations |
| BioProject |
PRJNA298343 |
| SRA |
SRP064663 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE73890_RAW.tar |
38.4 Mb |
(http)(custom) |
TAR (of MATRIX, TXT) |
| GSE73890_significant_differences_1repVs1rep.tar.gz |
107.4 Kb |
(ftp)(http) |
TAR |
| GSE73890_significant_differences_3repVs3rep.tar.gz |
478.6 Kb |
(ftp)(http) |
TAR |
| GSE73890_supplemental_readme.txt |
4.2 Kb |
(ftp)(http) |
TXT |
| GSE73890_supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx |
23.1 Kb |
(ftp)(http) |
XLSX |
| GSE73890_supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx |
22.8 Kb |
(ftp)(http) |
XLSX |
| GSE73890_supplemental_table_S1_all5Cprobes.xlsx |
126.7 Kb |
(ftp)(http) |
XLSX |
| GSE73890_yHiC-yJB1-R1_yHiC-yJB1-R4.log2ratio.matrix.gz |
3.2 Mb |
(ftp)(http) |
MATRIX |
| GSE73890_yHiC-yJB1-R1_yHiC-yJB1-R4.subtract.matrix.gz |
3.4 Mb |
(ftp)(http) |
MATRIX |
| GSE73890_yHiC-yJB1_sk1-rmv_genome_H-10000-iced.matrix.gz-n2r.txt.gz |
9.0 Mb |
(ftp)(http) |
TXT |
| GSE73890_yHiC-yJB2-R2_yHiC-yJB2-R4.log2ratio.matrix.gz |
3.3 Mb |
(ftp)(http) |
MATRIX |
| GSE73890_yHiC-yJB2-R2_yHiC-yJB2-R4.subtract.matrix.gz |
3.1 Mb |
(ftp)(http) |
MATRIX |
| GSE73890_yHiC-yJB2_sk1-rmv_genome_H-10000-iced.matrix.gz-n2r.txt.gz |
8.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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